The MLB 15 The Show developers released the following statement regarding the current state of their Online Franchises:
We have continued to see issues in certain Online Franchises. We believe we have finally identified the underlying causes and are taking steps to resolve them. Unfortunately, affected Online Franchises are not retrievable and will be removed from the system. We apologize for the inconvenience and remain endlessly appreciative of the community and its tremendous support for MLB 15 The Show.

These issues maybe be due to the amount of data in the online mode by many of the league’s created at launch. It looks like some of the earlier leagues may have to be removed.